PDB-4lzp: Structure of the TIR domain of the immunosuppressor BtpA from Brucella

ID or keywords:

Entry

Database: PDB / ID: 4lzp

Title

Structure of the TIR domain of the immunosuppressor BtpA from Brucella

Components

Putative uncharacterized protein

Keywords

IMMUNE SYSTEM /

TIR domain / Virulence factor Immuno suppressor /

MyD88 /

membrane

Function / homology

Function and homology information

NAD catabolic process / NADP+ nucleosidase activity /

NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating /

signal transduction / extracellular region
Similarity search - Function

Biological species

Brucella melitensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.15 Å

Authors

Kaplan-turkoz, B. / O'callaghan, D. / Vergunst, A. / Terradot, L.

Citation

Journal: Febs Lett. / Year: 2013
Title: Structure of the Toll/interleukin 1 receptor (TIR) domain of the immunosuppressive Brucella effector BtpA/Btp1/TcpB
Authors: Kaplan-turkoz, B. / Koelblen, T. / Felix, C. / Candusso, M.P. / O'callaghan, D. / Vergunst, A.C. / Terradot, L.

History

Deposition	Aug 1, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4lzp.cif.gz	251.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4lzp.ent.gz	206.7 KB	Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lz/4lzp ftp://data.pdbj.org/pub/pdb/validation_reports/lz/4lzp	HTTPS FTP

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Related structure data

Related structure data	3h16S S: Starting model for refinement
Similar structure data	2hf2-2 3gv0-d 5v41-1 5eb3-d 4y1r-d 4yna-1 6chk-d 3d8t-1 2zgk-1 4mlz-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (5)

Deposited unit

B: Putative uncharacterized protein

C: Putative uncharacterized protein

A: Putative uncharacterized protein

D: Putative uncharacterized protein

79.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Putative uncharacterized protein

A: Putative uncharacterized protein

defined by author&software
39.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Putative uncharacterized protein

D: Putative uncharacterized protein

defined by author&software
39.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.143, 73.928, 137.645
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	2

/ NCS ensembles :

ID
1
2

#1: Protein	Putative uncharacterized protein Mass: 19951.652 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: ATCC 23457 / Gene: BMEA_A0279 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C0RGW8

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.37 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal grow	Temperature: 293 K / Method: evaporation / pH: 5.5 Details: 20% Peg4K, 100mM Na Acetate, 200mM ammonium acetate, pH 5.5, EVAPORATION, temperature 293K

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Data collection

Diffraction

Mean temperature: 173 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.97626 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97626 Å / Relative weight: 1

Reflection

Resolution: 3.15→48.4 Å / Num. obs: 43030 / % possible obs: 98.1 % / Observed criterion σ(F): 1.1 / Observed criterion σ(I): 1.1 / R_merge(I) obs: 0.169

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Diffraction-ID	% possible all
3.15-3.32	3.6	0.668	1.5	1768	1	99.2
3.32-3.52	3.6	0.47	2.2	1683	1	98.4
3.52-3.76	3.6	0.34	3.1	1574	1	99.1
3.76-4.07	3.5	0.201	4.5	1486	1	98.6
4.07-4.45	3.6	0.145	6.1	1340	1	98.1
4.45-4.98	3.5	0.102	8.2	1235	1	97.8
4.98-5.75	3.5	0.106	7.4	1096	1	97.5
5.75-7.04	3.4	0.104	7.4	921	1	96.9
7.04-9.96	3.5	0.052	11.4	727	1	96.4
9.96-48.42	3.2	0.035	13.7	421	1	93.8

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3H16

3h16

Resolution: 3.15→48.4 Å / SU ML: 0.45 / σ(F): 0.09 / Phase error: 30.8 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.

	R_factor	Num. reflection	% reflection
R_free	0.2787	1083	4.76 %
R_work	0.2224	-	-
obs	0.2252	22751	97.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.15→48.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4669	0	0	0	4669

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4752
X-RAY DIFFRACTION	f_angle_d	0.992	6403
X-RAY DIFFRACTION	f_dihedral_angle_d	14.372	1737
X-RAY DIFFRACTION	f_chiral_restr	0.051	724
X-RAY DIFFRACTION	f_plane_restr	0.006	809

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
3.15-3.2937	0.3829	160	0.3304	2724	99
3.2937-3.4673	0.3702	115	0.3023	2769	99
3.4673-3.6844	0.3687	128	0.2795	2706	98
3.6844-3.9688	0.3206	127	0.2412	2751	99
3.9688-4.368	0.2545	143	0.2092	2696	98
4.368-4.9994	0.2216	132	0.1717	2720	98
4.9994-6.2966	0.2055	140	0.1865	2690	97
6.2966-48.4285	0.2358	138	0.1639	2612	95

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.7875	1.2726	-0.2562	6.2234	-0.1697	5.5314	-0.0643	0.0173	0.5711	0.2709	0.4251	0.7804	0.0326	-1.144	-0.3359	0.3937	-0.1325	0.0766	0.6973	0.0095	0.6426	31.894	-0.005	-56.983
2	3.0327	1.9169	-0.6785	3.9844	-0.9346	1.36	-0.1598	0.0531	0.3172	0.1701	-0.1093	0.3494	-0.1799	-0.4828	0.3823	0.7005	-0.2016	0.0383	0.6512	-0.313	0.6835	33.878	0.36	-58.176
3	2.021	2.8387	-6.265	2.0083	-3.1165	2.0168	0.3869	-1.0239	-0.7591	0.6353	-0.1171	-0.4111	0.2932	-0.3206	-0.1568	0.6651	-0.0341	-0.059	0.5721	0.0963	0.6902	23.47	-5.912	-66.021
4	3.8852	0.6881	-0.3193	4.4138	1.2819	3.259	0.22	0.6893	-0.3836	0.2206	-0.3192	0.8059	-0.2819	-0.5782	0.1241	0.3555	-0.0099	-0.0388	0.6693	-0.1108	0.4434	22.796	-2.639	-53.751
5	2.001	9.0202	2.645	8.8164	-3.1654	4.3063	0.1109	-0.6109	-0.3108	0.8634	-0.0231	-0.4199	0.3135	0.1573	0.0198	0.567	-0.1343	-0.0416	0.2341	-0.0386	0.9063	15.004	-9.03	-56.463
6	0.6508	0.0984	-0.9108	0.4438	0.1717	1.1516	0.2239	-1.321	-0.4913	0.6679	0.0908	-0.8142	0.2602	0.9946	0.0096	1.0287	-0.122	-0.2034	-2.1682	-0.4023	0.7237	26.517	-12.262	-54.804
7	4.5253	2.6	0.0558	3.2062	1.0183	3.9861	-0.0496	0.5767	-0.5566	-0.2805	0.2566	-0.7286	0.0879	0.4456	-0.1839	0.3874	-0.0432	-0.0963	0.5559	-0.2001	0.5928	17.729	-7.737	-44.053
8	2.491	-1.6237	-2.5285	4.4832	-0.5066	3.9756	-0.8521	-0.0311	-0.3978	0.1335	-0.0968	-1.019	0.0547	0.795	0.9421	0.3845	0.0353	-0.0154	0.7166	0.203	0.5951	30.27	-10.479	-44.389
9	3.8813	0.2598	1.7027	8.0405	-3.2086	7.5871	0.2901	-0.3499	-0.5217	0.3474	0.0189	0.4302	0.5196	-0.7808	-0.3232	0.5799	-0.0619	0.0543	0.6504	0.0746	0.825	39.882	-10.939	-51.245
10	0.1032	-0.0545	-0.3371	0.0754	0.2665	1.1585	-0.2212	-0.3527	0.2775	1.414	0.4363	0.1321	-0.4756	-0.3786	-0.2825	0.9814	-0.067	0.05	1.234	-0.1016	0.4694	17.507	-7.723	-12.5
11	5.54	-0.6833	-1.3941	1.3585	-1.9444	5.2534	0.4787	-0.2711	-1.1376	-0.3595	-0.1779	0.1432	0.8558	-0.0985	-0.3876	0.6358	-0.0126	-0.1607	0.5315	0.036	0.5085	19.941	1.405	-26.047
12	7.2992	2.3357	-1.1905	2.0644	-0.2602	1.367	0.4264	-1.6188	-1.2195	0.5515	-0.2637	-0.1318	0.4404	-0.1398	-0.2207	0.4467	-0.0782	-0.1071	0.4947	0.1531	0.6781	17.616	-0.858	-21.501
13	1.9902	1.3522	6.457	5.8	3.2179	5.1081	0.5571	-1.186	-0.5924	0.7883	-0.0604	1.3139	0.2284	-1.2091	-0.2031	0.6094	-0.0454	0.0951	1.4124	0.067	0.5212	28.559	-0.474	-13.593
14	4.1449	-1.4693	-1.1344	1.9318	-1.6505	3.3633	0.1032	0.558	-0.0607	-0.168	-0.0431	0.3392	0.5646	-0.431	-0.1124	0.3742	-0.0461	-0.0939	0.5403	0.19	0.4071	27.4	0.573	-28.25
15	7.2437	-3.5995	0.1919	2.0144	0.9906	5.2354	0.0073	-0.4857	-0.2192	1.0289	-0.0788	0.7605	-0.1963	-0.412	0.056	0.6888	-0.1412	0.014	1.5148	0.167	0.4775	36.747	5.038	-24.662
16	4.6032	0.2058	1.5882	1.864	-1.2667	4.1544	-0.6134	-0.5256	0.6653	0.1723	0.0757	0.4485	-0.3498	-0.8106	0.4895	0.3677	0.1039	0.0286	0.7133	-0.005	0.4407	30.845	-6.306	-26.077
17	2.0271	0.8938	1.6833	1.8912	0.4379	2.0048	0.2267	-0.6212	0.7526	-0.2925	0.5298	0.3787	-0.0329	-0.1358	-0.3943	0.4851	0.0922	0.0271	0.6595	-0.0391	0.5015	38.161	-1.695	-34.823
18	1.8334	2.1645	-0.2789	3.604	-0.3039	4.4846	0.1206	0.0473	0.0705	0.5143	-0.211	0.1414	0.0991	0.1039	0.0653	0.4689	-0.1907	-0.1856	0.4206	0.2452	0.815	26.421	-10.654	-33.645
19	8.5669	2.2219	1.511	2.0303	4.3191	1.9988	-0.0613	0.6013	0.4689	-0.5567	0.9443	-0.3857	0.2814	-0.0656	-0.4295	0.6038	0.0289	-0.1028	0.4487	0.2103	0.3869	18.679	-14.677	-25.955
20	3.9026	-0.6096	-3.7092	2.6768	0.5882	2.027	-0.253	0.3821	-1.1196	0.2927	-0.376	0.0612	0.0105	-0.2338	0.2854	0.5003	-0.0784	-0.0528	0.5984	-0.0164	0.6593	-2.388	17.597	-31.939
21	5.1388	0.4481	-1.418	3.9002	-1.9665	4.7464	-0.2468	-0.1132	0.5836	-1.1136	0.5162	-0.7806	0.3604	0.1136	-0.3144	0.5954	-0.1099	0.0758	0.9418	-0.1275	0.6362	-1.459	2.341	-8.357
22	4.3489	-0.8094	-0.8262	6.3564	1.612	3.7591	-0.5871	0.3139	0.584	-0.9935	-0.2673	0.4038	-1.2241	-0.3916	0.7297	0.7373	0.2261	-0.148	1.5394	-0.0042	0.6903	2.449	-2.895	-13.607
23	5.3478	-0.8863	-1.7348	4.3136	1.2125	7.763	0.1573	0.4823	0.4485	-0.8121	0.5149	-0.7593	-0.6502	-0.6679	-0.4585	0.5662	-0.0628	-0.0608	0.464	0.1339	0.7124	-10.628	0.431	-10.845
24	6.0238	0.0005	-3.2425	0.0996	-0.4725	3.8438	-0.2199	-0.2915	-0.2388	-0.2759	0.3069	0.2168	0.2279	-0.973	-0.1291	0.4708	-0.0096	-0.1009	0.8677	-0.1694	0.6674	-16.572	6.798	-12.119
25	4.1237	-1.3226	-1.4665	2.4562	1.1439	3.4295	0.2667	0.0154	-0.2743	-0.2118	-0.3166	0.2403	-0.042	-0.2374	0.129	0.4855	0.0253	-0.1489	0.4427	-0.1613	0.5561	-6.596	7.301	-22.51
26	5.4881	-1.3856	1.5001	4.0146	0.5781	0.6571	0.318	1.4747	-0.3098	-1.0187	0.0042	0.215	0.0009	-0.095	0.0211	0.6531	0.2604	-0.1671	1.06	-0.3955	0.7689	-13.727	4.198	-55.167
27	3.8469	-2.7969	-1.3974	7.9126	-1.5679	3.0502	-0.442	-0.5712	-0.6204	0.6109	-0.2441	0.552	0.1304	-1.106	0.4067	0.5832	0.1417	-0.0962	0.787	-0.2178	0.6301	-15.205	-6.092	-40.397
28	2.665	-2.9858	-0.0885	4.9514	-0.5326	1.8394	0.3295	0.7003	-0.3786	-0.8851	0.1115	0.2245	-0.0602	-1.5562	0.0095	0.5661	-0.0004	-0.2727	0.7404	-0.207	0.7847	-16.33	-1.143	-47.995
29	2.8146	-1.1479	0.8835	4.0505	0.6564	3.9589	0.3674	1.2406	-0.1231	-1.3943	-0.6198	-0.2258	-0.2935	-0.0145	0.1697	0.9892	0.2773	-0.1155	0.7645	-0.2098	0.5469	-6.254	-0.349	-53.114
30	4.978	-0.7581	0.659	6.8642	1.715	0.861	-0.5612	0.0359	-0.6301	0.426	0.0934	0.2324	0.5269	0.0376	0.251	0.4704	0.0121	-0.0944	0.3321	-0.1265	0.5285	-3.375	-8.631	-39.55
31	1.9972	-8.3968	-2.9517	8.0806	-2.6265	8.8388	0.2148	0.2092	0.1647	-0.3079	0.0039	-0.1366	-0.7451	-0.0738	0.0774	0.4292	-0.0019	-0.0376	0.8692	-0.0738	0.6008	4.486	-2.555	-46.76
32	1.6334	-1.6601	2.3207	3.6445	0.2896	7.0834	0.3774	-0.4155	0.6555	-0.811	-0.5436	-0.619	-0.3596	0.6438	0.2487	0.3808	-0.1989	0.0462	0.8571	-0.1617	0.738	-3.315	5.84	-46.406
33	3.3023	-4.4397	-1.5067	2.0833	1.3787	2.0703	0.094	-1.0184	-0.2076	0.5744	0.766	0.0422	0.2607	0.2273	-0.9898	0.59	0.0585	-0.0093	0.517	-0.0268	0.5986	-0.002	-1.566	-32.487
34	4.9123	-1.2891	1.8349	4.058	-1.4573	1.2454	-0.6364	-0.1281	0.4729	-0.5779	0.1857	-0.7472	0.0865	-0.318	0.3307	0.4327	0.0119	0.0118	0.3677	-0.063	0.423	-2.977	6.446	-36.89
35	9.1856	1.4533	-3.5185	2.0145	-2.1026	2.007	-0.0335	0.2534	0.6216	-0.0038	-0.0421	0.0797	-0.8219	-0.1352	-0.0506	0.7566	-0.0577	-0.1801	0.395	-0.0483	0.4345	-15.057	12.614	-43.703

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 143 through 158 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 159 through 185 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 186 through 196 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 197 through 214 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 215 through 221 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 222 through 236 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 237 through 253 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 254 through 263 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 264 through 275 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 143 through 145 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 146 through 158 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 159 through 185 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 186 through 198 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 199 through 210 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 211 through 220 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 221 through 240 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 241 through 253 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 254 through 263 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 264 through 275 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 100 through 132 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 133 through 153 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 154 through 179 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 180 through 211 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 212 through 231 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 232 through 275 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 141 through 149 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 150 through 158 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 159 through 185 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 186 through 204 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 205 through 214 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 215 through 222 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 223 through 236 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 237 through 247 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 248 through 263 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 264 through 275 )

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